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High-speed multiple sequence alignment on a reconfigurable platform.

Tim Oliver1, Bertil Schmidt, Douglas Maskell

  • 1School of Computer Engineering, Nanyang Technological University, Singapore. tim.oliver@gmail.com

International Journal of Bioinformatics Research and Applications
|December 1, 2007
PubMed
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We present a novel approach for fast multiple sequence alignment (MSA) using reconfigurable hardware. This method significantly reduces computation time for large sequence datasets, benefiting biological research.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Hardware Acceleration

Background:

  • Multiple sequence alignment (MSA) is crucial for biological sequence analysis.
  • Current MSA methods are computationally intensive, requiring hours for large datasets.
  • The exponential growth of sequence databases necessitates faster alignment techniques.

Purpose of the Study:

  • To develop a high-performance, low-cost approach for computing MSAs.
  • To accelerate the MSA process using reconfigurable hardware platforms.
  • To address the time constraints faced by biologists due to large sequence databases.

Main Methods:

  • Implementation of a linear systolic array architecture.
  • Utilizing dynamic programming for pairwise sequence distance computations.

Related Experiment Videos

  • Leveraging Field-Programmable Gate Arrays (FPGAs) for hardware acceleration.

    • Main Results:

    • Significant runtime savings achieved for MSA computation.
    • Demonstrated high performance on a standard FPGA platform.
    • A cost-effective solution for accelerating bioinformatics workflows.

    Conclusions:

    • The proposed systolic array on FPGAs offers a viable solution for rapid MSA.
    • This approach can significantly improve the efficiency of analyzing large biological sequence data.
    • Accelerated MSA computation empowers faster biological discovery.